Data Visualization and Exploration v2
Joey Hulbert
1/1/2022
Purpose
The purpose of this document is to track and provide instructions for reproducing the analyses of the Wester Redcedar Dieback Map project data.
Approach
The overall approach is to model empirical data collected by community scientists with ancillary environmental data (climate, topographic, and soils) to identify important predictors of western redcedar dieback.
Open questions
The below bullets are questions or comments that should be resolved before final analyses
- Considerations
- Should we filter data to remove GPS points with poor accuracy?
- Data averaged over last decade or last 30 years?
- Better approach to calculate topographic data?
- Should we restrict data to Washington and Oregon because that is where soils data is available.
- Should we look at data from last decade only or also from last 30 years?
Notes
- Important notes to consider when visualizing these data.
- Observations are filtered to only include those with Soils Data
- Data is filtered to show most common symptoms only.
Data
The data used in the below visualizations are described in the Data Wrangle folder.
## # A tibble: 11 x 2
## # Groups: field.tree.canopy.symptoms [11]
## field.tree.canopy.symptoms n
## <fct> <int>
## 1 Branch Dieback or 'Flagging' 19
## 2 Browning Canopy 19
## 3 Extra Cone Crop 2
## 4 Healthy 403
## 5 Multiple Symptoms (please list in Notes) 17
## 6 New Dead Top (red or brown needles still attached) 33
## 7 Old Dead Top (needles already gone) 83
## 8 Other (please describe in Notes) 8
## 9 Thinning Canopy 118
## 10 Tree is dead 37
## 11 Yellowing Canopy 10## # A tibble: 5 x 2
## # Groups: field.tree.canopy.symptoms [5]
## field.tree.canopy.symptoms n
## <fct> <int>
## 1 Healthy 403
## 2 New Dead Top (red or brown needles still attached) 33
## 3 Old Dead Top (needles already gone) 83
## 4 Thinning Canopy 118
## 5 Tree is dead 37## # A tibble: 2 x 2
## # Groups: field.tree.canopy.symptoms [2]
## field.tree.canopy.symptoms n
## <fct> <int>
## 1 Healthy 403
## 2 Unhealthy 346Data Visualization
Climate
Decade 2011-2020
MAT
Symptoms
Site Severity
Size Class
MAP
AHM
SHM
Filtered SHM <200
MSP
CMD
Eref
TOPO Data
Aspect
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
Slope
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
Elevation
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
Topo & Climate
Slope
CMD
## Warning: Removed 4 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 4 rows containing non-finite values (stat_smooth).
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 4 rows containing non-finite values (stat_smooth).
Elevation
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 4 rows containing non-finite values (stat_smooth).
Soils Data
Bedrock Depth
## Warning: Removed 621 rows containing non-finite values (stat_boxplot).
drclasscd
drclasswettest
hydgrpdcd
slopegradwta
## Warning: Removed 33 rows containing non-finite values (stat_boxplot).
niccdcdpct
## Warning: Removed 3 rows containing non-finite values (stat_boxplot).
Binary Data
Climate
MAT
Site Severity
Size Class
MAP
AHM
SHM
Filtered SHM <200
MSP
CMD
Eref
Topo
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning: Removed 6 rows containing non-finite values (stat_smooth).
## Warning: Removed 6 rows containing non-finite values (stat_boxplot).
Soils
Bedrock Depth
## Warning: Removed 688 rows containing non-finite values (stat_boxplot).
drclasscd
drclasswettest
hydgrpdcd
slopegradwta
## Warning: Removed 38 rows containing non-finite values (stat_boxplot).
niccdcdpct
## Warning: Removed 4 rows containing non-finite values (stat_boxplot).
component_taxgrtgroup
#### component_taxpartsize
## NULL
muaggatt_wtdepaprjunmin
Water Table Depth - April - June - Minimum
## int [1:749] 45 23 NA NA NA NA 0 NA NA NA ...## Warning: Removed 441 rows containing non-finite values (stat_boxplot).